Browse code

added a few items to the TODOs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38459 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 03/04/2009 09:37:26
Showing 4 changed files

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@@ -84,3 +84,7 @@ and crlmmIllumina() in crlmm-illumina.R)
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 2009-04-01 Matt Ritchie - committed version 1.0.67
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 * added import statement for normalize.quantiles
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+2009-04-01 R.Scharpf - committed version 1.0.69
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+* added a few items to the crlmm TODOs
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@@ -1,7 +1,7 @@
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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for SNP 5.0 and 6.0 arrays.
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-Version: 1.0.68
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+Version: 1.0.69
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 Date: 2008-12-30
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 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>
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 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>
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@@ -953,7 +953,6 @@ biasAdj <- function(plateIndex, envir, priorProb){
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 	plate <- envir[["plate"]]
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 	if(missing(priorProb)) priorProb <- rep(1/4, 4) ##uniform
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 	emit <- array(NA, dim=c(nrow(A), ncol(A), 10))##SNPs x sample x 'truth'	
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 	lA <- log2(A)
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 	lB <- log2(B)	
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 	X <- cbind(lA, lB)
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@@ -995,7 +994,11 @@ biasAdj <- function(plateIndex, envir, priorProb){
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 	hemDel <- apply(hemDel, c(1,2), sum)
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 	norm <- apply(norm, c(1, 2), sum)
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 	amp <- apply(amp, c(1,2), sum)
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-
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+	total <- hemDel + norm + amp
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+	hemDel <- hemDel/total
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+	norm <- norm/total
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+	amp <- amp/total
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+	envir[["posteriorProb"]] <- list(hemDel=hemDel, norm=norm, amp=amp) 
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 	tmp <- array(NA, dim=c(nrow(A), ncol(A), 4))
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 	tmp[, , 1] <- homDel
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 	tmp[, , 2] <- hemDel
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@@ -6,6 +6,15 @@
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 - Allele plots
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 - M v S plots
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+R. Scharpf (after next release)
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+- crlmm should return a SnpSet object with elements A, B, calls, and
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+  confs in the assayData when save.it=TRUE.  These objects can be very
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+  big, so...  
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+- crlmm function should have an option to return nothing and write to
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+  file a SnpSet object for each chromosome.  This would help the copy
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+  number part that runs by chromosome
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 #####################################
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 ### FOR CNRMA